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  while (<INPUT2>) {
    $_ =~ s/[\r\n]+\z//s; # I don't use chomp, sorry
...
    my $origin = $origins{$contig_id};
    print RESULTS "$bioC\t$origin\t$pip\n";
  }

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  my $origin = $origins{$contig_id};
  if ( ! defined( $origin ) ) {
    die( "No mapping for \"$contig_id\" found in origins table" );
  }